In a gene expression array study comparing signatures of chronic liver diseases with hepatocellular carcinoma, we revealed a molecular signature that separates these patients for their risk of developing advanced disease. Epithelial cell adhesion molecule (EpCAM) was identified as the lead gene in this signature and silencing of this gene resulted in growth suppression of hepatocellular carcinoma (HCC) cells. We have also analyzed the gene expression differences among EpCAM positive or negative HCC. We found that EpCAM could significantly differentiate HCC into two subtypes that resembled liver lineages. In particular, EpCAM-positive HCC displayed distinct features of hepatic stem/progenitor cells including an activation of the wnt-beta catenin pathway. Meanwhile, EpCAM-negative HCC displayed features of mature hepatocytes. We also found that HCC could be further stratified into four distinct subtypes with the additional assessment of alpha-fetoprotein status. These four subtypes were associated with prognostic outcome of HCC and cells double positive for EpCAM and alpha-fetoprotein had the worst prognosis. Furthermore, these subtypes resembled certain stages of liver lineages and EpCAM/alpha-fetoprotein-positive cells displayed a distinct molecular signature with features of hepatic stem/progenitor cells. Moreover, these cells, characterizing a poor prognostic HCC subtype, were capable of initiating highly invasive HCC in in-vitro and in-vivo models. This work suggests that EpCAM and alpha-fetoprotein are useful diagnostic markers for HCC which can be used as a convenient classification system for prognosis. Furthermore, EpCAM and alpha-fetoprotein may act as downstream molecules to maintain HCC stemness and serve as good markers for HCC initiating cells. We have also recently explored whether the integrative genomic profiling of a well-defined HCC subset of extreme EpCAM+ AFP+ could uncover survival-related driver genes in HCC. This analysis revealed that YY1-associated protein 1 (YY1AP1) is a critical oncoprotein specifically activated in EpCAM+AFP+ HCC. YY1AP1 silencing eliminates oncogene addiction by altering the chromatin landscape while YY1AP1 expression promotes HCC proliferation and is required for the maintenance of stem cell features. Thus YY1AP1 may serve as a key molecular target for EpCAM+ AFP+ HCC subtype. We also invetsigated the mechanism by which EpCAM is elevated in hepatocellular carcinoma subtypes with stem/progenitor cell features. We found that the activation of wnt-beta-catenin pathway regulates EpCAM expression. We demonstrate that EpCAM is a biosensor for wnt-beta-catenin signaling and is transcriptionally up-regulated by this pathway through direct Tcf binding element interactions. Our data suggest that the convergence of EpCAM expression and wnt-beta-catenin signaling functions to maintain hepatocellular carcinoma cell growth. Inhibition of hepatocellular carcinoma cell growth could be achieved through blockade of EpCAM/wnt-beta-catenin signaling in EpCAM-positive hepatocellular carcinoma cells. With these findings, we propose that EpCAM/wnt-beta-catenin signaling functions to maintain hepatocellular carcinoma stem cell growth and that EpCAM expression-based classification of hepatocellular carcinoma could be useful in clinical settings to stratify hepatocellular carcinoma patients who may benefit from beta-catenin/EpCAM adjuvant therapies. The cancer stem cell marker, EpCAM, is an important indicator of Wnt/beta-catenin signaling activation and a functional component of hepatocellular tumor-initiating cells. A high-throughput screening assay was developed to identify inhibitors of EpCAM-dependent growth of hepatocellular carcinoma (HCC) cells. EpCAM(+) and EpCAM(-) HCC cell lines were assessed for differential sensitivity to a Wnt/beta-catenin pathway inhibitor. Libraries comprising 22 668 pure compounds and 107 741 crude or partially purified natural product extracts were tested, and 12 pure compounds and 67 natural product extracts were identified for further study. Three active compounds and the positive control were further characterized in terms of effects on EpCAM expression. Treatment of EpCAM(+) Hep3B cells resulted in loss of EpCAM expression as assessed by flow cytometry. This reduction was incomplete, but resulted in generation of cell populations expressing lower levels of EpCAM. Sublethal concentrations reduced median EpCAM expression and preceded growth inhibition suggesting that a threshold of EpCAM expression may be required for growth of EpCAM-dependent cells. The identification of compounds with a variety of possible molecular targets suggests a likelihood of multiple mechanisms for modulation of EpCAM-dependent cell growth. MicroRNAs are endogenous small noncoding RNAs that regulate gene expression with functional links to tumorigenesis. A global microRNA microarray approach was used to explore whether certain microRNAs were associated with hepatocellular carcinoma stem cells. We found that the conserved microRNA-181 family members were up-regulated in hepatoceullar carcinoma stem cells. Inhibition of microRNA-181 led to a reduction in number and tumor initiating activity of hepatocellular carcinoma stem cells while addition of microRNA-181 led to an enrichment of this cell type. In further studies, we showed that microRNA-181 could directly target transcriptional regulators of differentiation in the liver and an inhibitor of wnt-beta-catenin signaling. In addition, we have recently shown that Wnt/beta-catenin signaling transcriptionally activates microRNA-181s in HCC. These results suggest a novel regulatory link between microRNA-181 family members, Wnt/beta catenin signaling and liver cancer stem cells and implies that molecular targeting of microRNA-181 or Wnt/beta-catenin signaling may eradicate hepatocellular carcinoma. We have also recently explored whether specific microRNAs exist in hepatic cancer stem cells (CSCs) that are not expressed in normal hepatic stem cells by assessing the microRNA transcriptome of HCC specimens by small RNA deep sequencing. We found that miR-150, miR-155, and miR-223 were preferentially highly expressed in EpCAM+ HCC cells and their gene surrogates were associate with patient prognosis. Further studies showed that suppressing miR-155 resulted in reduction of EpCAM+ HCC cells, reduced HCC tumorigenicity and shortened overall survival and time to recurrence of HCC patients. Thus, miR-155 was highly elevated in EpCAM1 HCC cells and might serve as a molecular target to eradicate the EpCAM+ CSC population in human HCCs. We have recently assessed molecular signatures related to HCC stemness and outcome in intrahepatic cholangiocarcinoma (ICC). Using Affymetrix mRNA and Nanostring microRNA microarrays, Asian ICC cases could be segregated into two main subgroups, one of which shared gene expression signatures with previously identified HCC with stem cell gene expression traits. Integrative analyses of the ICC-specific mRNA and microRNA expression profiles revealed that a common signaling pathway linking miR-200c signaling to epithelial-mesenchymal transition (EMT) was preferentially activated in ICC with stem cell gene expression traits. Inactivation of miR-200c resulted in an induction of EMT while activation of miR-200c led to a reduction of EMT including a reduction of cell migration and invasion. We also found that NCAM1, a known hepatic stem/progenitor cell marker, was a direct target of miR-200c. Our results indicate that ICC and HCC share common stem-like molecular characteristics and poor prognosis. Our work suggests that specific components of EMT may be exploited as critical biomarkers and clinically relevant therapeutic targets for an aggressive form of stem cell-like ICC.